swash: Swash-Backwash Model for the Single Epidemic Wave

In swash: Swash-Backwash Model for the Single Epidemic Wave

Swash-Backwash Model for the Single Epidemic Wave

Description

Analysis of regional infection/surveillance data using the Swash-Backwash Model for the single epidemic wave by Cliff and Haggett (2006)

Usage

swash(
  data, 
  col_cases, 
  col_date, 
  col_region
  )

Arguments

data	data.frame with regional infection data
col_cases	Column containing the cases (numeric)
col_date	Column containing the time points (e.g., days)
col_region	Column containing the unique identifier of the regions (e.g., name, NUTS 3 code)

Details

The function performs the analysis of the input panel data using the Swash-Backwash Model. The output is an object of class "sbm". The results can be viewed using summary(sbm). The user must state panel data with daily infections.

Value

object of class sbm-class

Author(s)

Thomas Wieland

References

Cliff AD, Haggett P (2006) A swash-backwash model of the single epidemic wave. Journal of Geographical Systems 8(3), 227-252. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1007/s10109-006-0027-8")}

Smallman-Raynor MR, Cliff AD, Stickler PJ (2022) Meningococcal Meningitis and Coal Mining in Provincial England: Geographical Perspectives on a Major Epidemic, 1929–33. Geographical Analysis 54, 197–216. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1111/gean.12272")}

Smallman-Raynor MR, Cliff AD, The COVID-19 Genomics UK (COG-UK) Consortium (2022) Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020–December 2021. Epidemiology and Infection 150, e145. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1017/S0950268822001285")}.

See Also

sbm-class

Examples

data(COVID19Cases_geoRegion)
# Get SWISS COVID19 cases at NUTS 3 level

COVID19Cases_geoRegion <- 
  COVID19Cases_geoRegion[!COVID19Cases_geoRegion$geoRegion %in% c("CH", "CHFL"),]
# Exclude CH = Switzerland total and CHFL = Switzerland and Liechtenstein total

COVID19Cases_geoRegion <- 
  COVID19Cases_geoRegion[COVID19Cases_geoRegion$datum <= "2020-05-31",]
# Extract first COVID-19 wave

CH_covidwave1 <- 
  swash (
    data = COVID19Cases_geoRegion, 
    col_cases = "entries", 
    col_date = "datum", 
    col_region = "geoRegion"
    )
# Swash-Backwash Model for Swiss COVID19 cases
# Spatial aggregate: NUTS 3 (cantons)

summary(CH_covidwave1)
# Summary of Swash-Backwash Model

plot(CH_covidwave1)
# Plot of Swash-Backwash Model edges and total epidemic curve

swash documentation built on June 8, 2025, 1:25 p.m.